This has come up a few times before and its a great way to promote gameplay in the MA's. If you want realism you fly scenarios not the MA's anyway. HTC makes no pretense of the MA's being ww2 simulators, rather, its a game using ww2 class vehicles.
The idea of using bomber perks to build bases is a great one. There is currently no economy for bomber perks. This makes sense as bombers destroy object so why not let bomber perks help build objects? The current game play model is rather limited and stagnant. Dynamic bases greatly increase teamwork and strategic action.
I would suggest the following; Bases are limited in distance and location from each other and static bases. From a map point of view, one could define exclusion zones where non could be built and range limits from each other.
Bases would be built by c47's, lvts, skdfs or m3's dropping base supplies. Lets use 100 perks as an starting point. A higher starting point might initially be used to burn up all those 10's of thousands of currently useless bomber perks. As with the current model you would only lose perks if you lost the plane. From a programing point of view, each drop adds something to the base while damage takes it away. Perhaps the something close to the current model or where base supplies are applied to repairing current damage and additional "points" are applied to the next item of added capacity. Player made bases are only supplied via base supplies so once a base is discovered getting supplies there will become more risky. Having to supply individual amounts of fuel or bombs would be problematic since you can't control who ups with them. One can only imagine the whining of those who supply some fuel only to have that fuel used up before they can use it by someone else.